Schejter, E D, L S Rose, M A Postner, and E Wieschaus. 1992. “Role of the Zygotic Genome in the Restructuring of the Actin Cytoskeleton at the Cycle-14 Transition During Drosophila Embryogenesis.”. Cold Spring Harb Symp Quant Biol 57: 653-9.

Schumer, Molly, Rongfeng Cui, Bastien Boussau, Ronald Walter, Gil Rosenthal, and Peter Andolfatto. (2013) 2013. “An Evaluation of the Hybrid Speciation Hypothesis for Xiphophorus Clemenciae Based on Whole Genome Sequences.”. Evolution 67 (4): 1155-68.

Schupbach, T, and E Wieschaus. 1998. “Probing for Gene Specificity in Epithelial Development.”. Int J Dev Biol 42 (3): 249-55.

Myers, Chad L, Camelia Chiriac, and Olga G Troyanskaya. 2009. “Discovering Biological Networks from Diverse Functional Genomic Data.”. Methods Mol Biol 563: 157-75.

Rowe, Kevin C, Sonal Singhal, Matthew D Macmanes, Julien Ayroles, Toni Lyn Morelli, Emily M Rubidge, Ke Bi, and Craig C Moritz. (2011) 2011. “Museum Genomics: Low-Cost and High-Accuracy Genetic Data from Historical Specimens.”. Mol Ecol Resour 11 (6): 1082-92.

Markstein, Michele, and Michael Levine. (2002) 2002. “Decoding Cis-Regulatory DNAs in the Drosophila Genome.”. Curr Opin Genet Dev 12 (5): 601-6.

Hendrix, David, Michael Levine, and Weiyang Shi. 2010. “MiRTRAP, a Computational Method for the Systematic Identification of MiRNAs from High Throughput Sequencing Data.”. Genome Biol 11 (4): R39.

Gresham, David, Maitreya Dunham, and David Botstein. (2008) 2008. “Comparing Whole Genomes Using DNA Microarrays.”. Nat Rev Genet 9 (4): 291-302.

Pollack, Jonathan R, Therese Sørlie, Charles M Perou, Christian A Rees, Stefanie S Jeffrey, Per E Lonning, Robert Tibshirani, David Botstein, Anne-Lise Børresen-Dale, and Patrick O Brown. (2002) 2002. “Microarray Analysis Reveals a Major Direct Role of DNA Copy Number Alteration in the Transcriptional Program of Human Breast Tumors.”. Proc Natl Acad Sci U S A 99 (20): 12963-8.

Lagha, Mounia, Jacques P Bothma, and Michael Levine. (2012) 2012. “Mechanisms of Transcriptional Precision in Animal Development.”. Trends Genet 28 (8): 409-16.

Pelham, Robert J, Linda Rodgers, Ira Hall, Robert Lucito, Ken C Q Nguyen, Nicholas Navin, James Hicks, et al. (2006) 2006. “Identification of Alterations in DNA Copy Number in Host Stromal Cells During Tumor Progression.”. Proc Natl Acad Sci U S A 103 (52): 19848-53.

Massouras, Andreas, Sebastian M Waszak, Monica Albarca-Aguilera, Korneel Hens, Wiebke Holcombe, Julien Ayroles, Emmanouil T Dermitzakis, et al. 2012. “Genomic Variation and Its Impact on Gene Expression in Drosophila Melanogaster.”. PLoS Genet 8 (11): e1003055.

Diehn, Maximilian, Ash A Alizadeh, Oliver J Rando, Chih Long Liu, Kryn Stankunas, David Botstein, Gerald R Crabtree, and Patrick O Brown. (2002) 2002. “Genomic Expression Programs and the Integration of the CD28 Costimulatory Signal in T Cell Activation.”. Proc Natl Acad Sci U S A 99 (18): 11796-801.

Stathopoulos, Angelike, and Michael Levine. (2002) 2002. “Whole-Genome Expression Profiles Identify Gene Batteries in Drosophila.”. Dev Cell 3 (4): 464-5.

Rossi, J M, D T Burke, J C Leung, D S Koos, H Chen, and S M Tilghman. (1992) 1992. “Genomic Analysis Using a Yeast Artificial Chromosome Library With Mouse DNA Inserts.”. Proc Natl Acad Sci U S A 89 (6): 2456-60.

Stathopoulos, Angelike, and Michael Levine. (2004) 2004. “Whole-Genome Analysis of Drosophila Gastrulation.”. Curr Opin Genet Dev 14 (5): 477-84.

Ayroles, Julien, Kimberly A Hughes, Kevin C Rowe, Melissa M Reedy, Sandra L Rodriguez-Zas, Jenny M Drnevich, Carla E Cáceres, and Ken N Paige. (2009) 2009. “A Genomewide Assessment of Inbreeding Depression: Gene Number, Function, and Mode of Action.”. Conserv Biol 23 (4): 920-30.

Stathopoulos, Angelike, Madeleine Van Drenth, Albert Erives, Michele Markstein, and Michael Levine. (2002) 2002. “Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo.”. Cell 111 (5): 687-701.

Markstein, Michele, Peter Markstein, Vicky Markstein, and Michael S Levine. (2002) 2002. “Genome-Wide Analysis of Clustered Dorsal Binding Sites Identifies Putative Target Genes in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 99 (2): 763-8.

Shi, Weiyang, Michael Levine, and Brad Davidson. (2005) 2005. “Unraveling Genomic Regulatory Networks in the Simple Chordate, Ciona Intestinalis.”. Genome Res 15 (12): 1668-74.

Corbett-Detig, Russell B, Jun Zhou, Andrew Clark, Daniel L Hartl, and Julien Ayroles. (2013) 2013. “Genetic Incompatibilities Are Widespread Within Species.”. Nature 504 (7478): 135-7.

Troyanskaya, Olga G, Ora Arbell, Yair Koren, Gad M Landau, and Alexander Bolshoy. (2002) 2002. “Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity.”. Bioinformatics 18 (5): 679-88.

Katz, David J, Michael A Beer, John M Levorse, and Shirley M Tilghman. (2005) 2005. “Functional Characterization of a Novel Ku70 80 Pause Site at the H19 Igf2 Imprinting Control Region.”. Mol Cell Biol 25 (10): 3855-63.

Butte, Atul J, Indra Neil Sarkar, Marco Ramoni, Yves Lussier, and Olga Troyanskaya. 2009. “Selected Proceedings of the First Summit on Translational Bioinformatics 2008.”. BMC Bioinformatics 10 Suppl 2: I1.

Vukmirovic, O G, and S M Tilghman. (2000) 2000. “Exploring Genome Space.”. Nature 405 (6788): 820-2.

Christiaen, Lionel, Eileen Wagner, Weiyang Shi, and Michael Levine. (2009) 2009. “The Sea Squirt Ciona Intestinalis.”. Cold Spring Harb Protoc 2009 (12): pdb.emo138.

Berman, Benjamin P, Yutaka Nibu, Barret D Pfeiffer, Pavel Tomancak, Susan E Celniker, Michael Levine, Gerald M Rubin, and Michael B Eisen. (2002) 2002. “Exploiting Transcription Factor Binding Site Clustering to Identify Cis-Regulatory Modules Involved in Pattern Formation in the Drosophila Genome.”. Proc Natl Acad Sci U S A 99 (2): 757-62.